Mercurial > repos > recetox > ramclustr
changeset 2:eac0e6feb850 draft
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit d4a601c637b18f18a5cda9111208559e72d12657"
| author | recetox |
|---|---|
| date | Mon, 17 Jan 2022 16:28:54 +0000 |
| parents | 15e173c5762c |
| children | 211cd88b5148 |
| files | ramclustr.xml |
| diffstat | 1 files changed, 50 insertions(+), 44 deletions(-) [+] |
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--- a/ramclustr.xml Thu Aug 19 07:17:15 2021 +0000 +++ b/ramclustr.xml Mon Jan 17 16:28:54 2022 +0000 @@ -14,52 +14,58 @@ <command detect_errors="aggressive"><![CDATA[ Rscript -e 'source("${__tool_directory__}/ramclustr_wrapper.R")' - #if $filetype.type_choice == "xcms": - -e 'x <- ramclustr_xcms( - input_xcms = "$filetype.input_xcms", - #else: - -e 'x <- ramclustr_csv( - ms="$filetype.ms_csv.ms", - idmsms="$filetype.ms_csv.idmsms", - feature_delimiter="$filetype.ms_csv.feature_delimiter", - sample_name_column = $filetype.ms_csv.sample_name_column, - retention_time_column= $filetype.ms_csv.retention_time_column, - #end if - sr = $filetype.required.sr, - deep_split = $filetype.required.deepSplit, - block_size = $filetype.required.blocksize, - mult = $filetype.required.mult, - hmax = $filetype.required.hmax, - collapse = $filetype.required.collapse, - use_pheno = $filetype.required.usePheno, - qc_inj_range = $filetype.required.qc_inj_range, - normalize = "$filetype.required.normalize", - min_module_size = $filetype.required.minModuleSize, - linkage = "$filetype.required.linkage", - mzdec = $filetype.required.mzdec, - cor_method = "$filetype.required.cor_method", - rt_only_low_n = $filetype.required.rt_only_low_n, - replace_zeros = $filetype.required.replace_zeros, - #if $filetype.type_choice == "xcms": - #if $filetype.optional.st - st = $filetype.optional.st, - #end if - #else: - st = $filetype.ms_csv.st, - #end if - #if $filetype.optional.maxt - maxt = $filetype.optional.maxt, - #end if - #if $filetype.optional.fftempdir - fftempdir = $filetype.optional.fftempdir, - #end if - #if $filetype.metadata.batch_order_qc - metadata_file = "${filetype.metadata.batch_order_qc}", - #end if - )' - -e 'store_output(x, "$result", "$method_metadata", $filetype.required.merge_msp, "$spec_abundance")' + -e 'source("${ramclustr_method}")' ]]> </command> + <configfiles> + <configfile name="ramclustr_method"> + store_output( + #if $filetype.type_choice == "xcms": + ramclustr_xcms( + input_xcms = "$filetype.input_xcms", + #else: + ramclustr_csv( + ms="$filetype.ms_csv.ms", + idmsms="$filetype.ms_csv.idmsms", + feature_delimiter="$filetype.ms_csv.feature_delimiter", + sample_name_column = $filetype.ms_csv.sample_name_column, + retention_time_column= $filetype.ms_csv.retention_time_column, + #end if + sr = $filetype.required.sr, + deep_split = $filetype.required.deepSplit, + block_size = $filetype.required.blocksize, + mult = $filetype.required.mult, + hmax = $filetype.required.hmax, + collapse = $filetype.required.collapse, + use_pheno = $filetype.required.usePheno, + qc_inj_range = $filetype.required.qc_inj_range, + normalize = "$filetype.required.normalize", + min_module_size = $filetype.required.minModuleSize, + linkage = "$filetype.required.linkage", + mzdec = $filetype.required.mzdec, + cor_method = "$filetype.required.cor_method", + rt_only_low_n = $filetype.required.rt_only_low_n, + replace_zeros = $filetype.required.replace_zeros, + #if $filetype.type_choice == "xcms": + #if $filetype.optional.st + st = $filetype.optional.st, + #end if + #else: + st = $filetype.ms_csv.st, + #end if + #if $filetype.optional.maxt + maxt = $filetype.optional.maxt, + #end if + #if $filetype.optional.fftempdir + fftempdir = $filetype.optional.fftempdir, + #end if + #if $filetype.metadata.batch_order_qc + metadata_file = "${filetype.metadata.batch_order_qc}", + #end if + ), + "$result", "$method_metadata", $filetype.required.merge_msp, "$spec_abundance") + </configfile> + </configfiles> <inputs> <conditional name="filetype"> <param name="type_choice" type="select" label="Choose input format:">